Dear Pierre,

I have tested PANDA with new version PSOM in 'background' mode.

However, when I used the 'background' mode, the software can only work in the bash/sh mode. When the shell is tcsh or csh, it cannot work.

I think this is a big problem, since some systems prefer csh/tcsh.

Then, if users process data with PANDA, they may encounter this problem.
Even though they can change the mode of system, however this may be a big obstacle for psychiatry and psychologists.

Hope for your reply.

Thanks very much.

Best

Zaixu

Dear Pierre,

I have made some changes to your script 'psom_run_script.m', and now it worked well in the csh/tcsh shell with 'background' mode.
I have replace the line 333 with line 334 and 335.
We can use sh to execute the script and don't use '.', and it will worked well in the csh/tcsh mode.

On the other way, I have changed the line 384, which is used to set the parameter of qsub.
I have added '-V' in this line.
With this parameter, all the terminal open in the background in the qsub mode will have the same environment variables with the current terminal. This is very important for us.

Thanks very much for your psom.

Wish you all the best.

Zaixu

Dear Zaixu,

Thanks a lot for reporting this problem, as well as finding a fix! I've committed your change to PSOM master:
 https://github.com/SIMEXP/psom/commit/a22b053f814159e24982dac0f1e580891edcd559

Re the -V option in qsub, I am afraid this may not be available universally. PSOM supports a range of different submission systems that all fall under the 'qsub' umbrella (msub, bsub, variants of qsub, condor). The right way to set up this type of site-specific configuration is to add

gb_psom_qsub_options = '-V';

line 29 of psom_gb_vars.m. It is also possible to specify this as an option for psom:

opt.qsub_options = '-V';

Best,

Pierre

Dear Pierre,

Thanks very much for your reply.
Yeah, I can specify the qsub options in the opt.qsub_options.

Best wishes

Zaixu